Software Name Version Classification PHENIX1.10_2155refinement PDB_EXTRACT3.27 data extraction XDSdata reduction Aimlessdata scaling PHASERphasing
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : 1DFBResolution : 1.70000520394→44.7076752723 Å / SU ML : 0.224743460608 / Cross valid method : THROUGHOUT / σ(F) : 1.34454775085 / Phase error : 22.9834555405 Stereochemistry target values : GeoStd + Monomer Library + CDL v1.2Rfactor Num. reflection % reflection Rfree 0.221877027097 1998 3.63808517999 % Rwork 0.179349882926 52921 - obs 0.180877855087 54919 96.5778598435 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 Å / Solvent model : FLAT BULK SOLVENT MODELDisplacement parameters Biso mean : 38.1791563834 Å2 Refinement step Cycle : LAST / Resolution : 1.70000520394→44.7076752723 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 3394 0 12 341 3747
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.0101717588849 3505 X-RAY DIFFRACTION f_angle_d1.06362218998 4776 X-RAY DIFFRACTION f_chiral_restr0.0622099096331 541 X-RAY DIFFRACTION f_plane_restr0.00680947514659 610 X-RAY DIFFRACTION f_dihedral_angle_d14.3758118642 1267
LS refinement shell Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)1.70000520394-1.7425 0.39464991286 111 0.353556494514 2930 X-RAY DIFFRACTION 75.4403373853 1.7425-1.7896 0.362193146933 121 0.309046787515 3219 X-RAY DIFFRACTION 83.688298672 1.7896-1.8423 0.308305854741 135 0.268791050586 3560 X-RAY DIFFRACTION 92.8858722976 1.8423-1.9018 0.278481816211 146 0.23631145236 3872 X-RAY DIFFRACTION 99.7765085672 1.9018-1.9697 0.284472761377 145 0.228589679803 3857 X-RAY DIFFRACTION 99.8752183679 1.9697-2.0486 0.223166654183 146 0.174418212026 3880 X-RAY DIFFRACTION 99.9751676186 2.0486-2.1418 0.213433461752 148 0.177983051754 3881 X-RAY DIFFRACTION 99.95038452 2.1418-2.2547 0.232551976425 146 0.182564786328 3874 X-RAY DIFFRACTION 99.9751305645 2.2547-2.396 0.20201774822 147 0.175670041138 3899 X-RAY DIFFRACTION 99.9505928854 2.396-2.581 0.237800989882 146 0.17999481004 3901 X-RAY DIFFRACTION 100 2.581-2.8407 0.25084099298 149 0.180173424458 3935 X-RAY DIFFRACTION 99.9755201958 2.8407-3.2516 0.210013850509 150 0.175286461353 3950 X-RAY DIFFRACTION 100 3.2516-4.0963 0.194552433658 150 0.158425681166 3979 X-RAY DIFFRACTION 100 4.0963-44.7076 0.193384770967 158 0.156144098928 4184 X-RAY DIFFRACTION 100
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 18) Hide large table ID L11 (°2 )L12 (°2 )L13 (°2 )L22 (°2 )L23 (°2 )L33 (°2 )S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2 )T12 (Å2 )T13 (Å2 )T22 (Å2 )T23 (Å2 )T33 (Å2 )Origin x (Å)Origin y (Å)Origin z (Å)1 4.91092814281 -2.47149993074 1.58782654842 5.07388020953 -2.01455040313 5.73884984062 0.0101002598943 -0.134187919173 -0.482842362692 0.0649331780048 0.210020161883 0.433103358475 0.129853707288 -0.367071195385 -0.36600015816 0.148536445154 0.0500413221988 0.058789390456 0.178552869804 0.0190698424716 0.189289847159 24.3609986668 43.6014435563 51.6249875229 2 3.22397996048 -0.561163120185 0.244046841952 2.35474631221 -0.486898188236 2.94101191806 -0.12720563205 -0.513038783243 -0.00211666471415 0.301782817514 0.140667637512 0.211012093226 -0.124117453952 -0.190121160552 -0.0353396917788 0.337044061815 0.1432011696 0.0764964238119 0.286698179162 0.022802699704 0.205722047891 28.1982091049 47.6958164352 60.4861901095 3 4.62793908721 -0.957709012672 2.1790425842 2.27602669352 -1.86270427312 2.05334240528 -0.148450093024 -0.770151746384 -0.21946019357 0.575572613568 0.198214499061 0.215623304152 -0.0807252544677 -0.0381643440528 0.295114317302 0.390868714351 0.154048213472 0.0769901608894 0.335621651381 0.0415940779583 0.180897337121 35.094116606 43.4264146777 62.2256459207 4 3.93887934238 -1.25233469038 0.042372490118 1.86593956183 -0.163807713231 5.25402633947 0.089842377302 -0.849202470065 0.178500170577 0.387612889117 0.171506549695 -0.212784421819 -0.378128007382 0.0665779867072 0.0489694539947 0.412515986995 0.138192762427 0.0616929864731 0.441408671672 0.0267555624796 0.221286201236 39.1685628331 44.3815507922 67.3744753486 5 0.470832346738 0.491567909812 -0.409256021869 0.515593910387 -0.167553315665 2.29835217495 -0.212772416619 0.0425368757425 0.0127419606965 0.385554550354 0.0740390822872 0.239368169766 -0.0500344807984 -0.205131067344 0.149429224866 0.194615396362 0.0754568151948 0.026778446565 0.220237965227 0.00542215521795 0.26153878165 24.3144395632 48.1840099935 40.9143653682 6 2.21286241078 -0.613445406092 -0.748803424074 3.14948231159 0.285821281217 2.81455707116 -0.0602661062606 0.124919144158 -0.0485903257818 -0.219178152513 0.0596963519257 -0.0927282644805 0.162547173288 -0.0534356713382 -0.00559001934859 0.0867248145568 -0.0232052437085 0.0116101960777 0.133792468734 -0.00789557477468 0.160790252229 32.2827396601 40.2087540766 25.4904373899 7 1.49385502619 0.990388818379 1.47883808513 2.10746012829 0.905553170688 1.74096725897 -0.0533887489114 0.294343568895 -0.193921952948 -0.382183011008 0.120525838873 0.118224283464 0.165088810522 -0.170416236139 0.473861746127 0.25260791668 -0.0568423609496 0.0534374300622 0.205315978133 0.0100319220898 0.234566024202 26.6949641284 33.8070275076 23.4000407237 8 0.739402021143 -0.655939647893 0.607639571795 1.65948847298 1.7513814344 8.68125010797 -0.0261415043148 0.561319692343 -0.305057084773 -0.5436731529 -0.00933303989281 0.376204001156 -0.403938996423 -0.121195019689 -0.101363509077 0.328671947701 -0.0722613785956 -0.0446655678936 0.396241051598 -0.0685243201905 0.285230569429 25.9000618462 37.2221525706 12.9410261602 9 5.01260753601 -3.58239519074 -3.40302001255 3.51511719847 3.26185576594 3.54061785405 -0.0398651127413 -0.016308096433 0.318823797574 0.300297566415 0.0661903909116 -0.442273373048 -0.364766009893 0.320649794347 -0.256620841903 0.292762154128 0.00323529434725 -0.0113981665458 0.201827755784 0.0200563585356 0.247120674887 55.8207450716 44.8778418551 49.5596727389 10 6.71525648764 5.39555805548 -4.17192657555 5.21117321559 -4.4855119856 4.23752151829 -0.127181262187 -0.688802600598 0.564121322204 0.604547675035 0.0437843053684 -0.200000756624 -1.07763817273 0.35013018459 -0.111318311325 0.5032205195 0.104354692437 -0.112784952278 0.348217066642 -0.133961198998 0.231143814759 53.2442791016 49.0483930134 71.071071085 11 4.89017357475 -0.247229764216 4.42106804966 1.55498492852 -1.03339968333 4.48756925719 0.0072982238883 0.0514317450357 -0.32239848624 0.115080958063 0.130345717485 0.11411199232 0.024786738099 -0.085288639294 -0.234287922033 0.228719617604 0.0711283918422 0.0190582874886 0.204519816207 -0.0184907467761 0.166989394418 44.4440202424 39.0172919342 53.7524772991 12 3.96659615782 -0.323009465119 -1.12254947338 4.43286234058 1.13334427369 4.91204572064 -0.28453793997 -0.329273497288 0.0275041631368 0.322036164567 0.184829263339 -0.184684563464 -0.122837124339 0.280894717152 0.107920610781 0.221103441312 0.0756850496622 -0.0608581034387 0.211139944573 0.00560554178786 0.18953198485 53.9582570426 38.1380588552 60.3448474249 13 1.35785764108 -0.392058938204 0.606798938153 1.26604402713 -0.907924123749 3.03260584701 0.0920982715392 0.0567940008094 0.160090198879 0.12645141507 -0.0448644449791 -0.303288242279 -0.181118682279 -0.0912865703456 -0.0578763342012 0.154437150397 0.056614935202 0.011206311608 0.165612136509 -0.00320542271706 0.187308430811 49.4582199835 42.4709815099 49.4595790751 14 2.26224274957 1.5280600301 0.902285355882 2.19341733782 -0.438041685185 4.89534204792 -0.0256956448681 0.622427628715 -0.0197409524826 -0.412686721991 0.1072514618 0.426086641723 0.348568212723 -0.466713714057 -0.188688384289 0.148825926173 -0.0549443531679 -0.0302506579958 0.273424137263 0.0115040952106 0.222348123289 32.4962427895 46.6230492783 15.0122482677 15 4.61450475482 -4.49777195875 4.49773316787 6.18001285352 -4.44435029356 5.38121683827 -0.234072459376 -0.173466248239 0.0968289834961 -0.0405480669605 0.00242637049443 -0.311387996494 -0.0370911905263 0.268087054609 0.226269200141 0.0857424644745 0.0067412748145 0.0544374834021 0.192078270018 -0.0175109418648 0.127210086945 45.1739495176 48.0023750028 23.452956824 16 1.54961608455 0.546736082808 0.0601942168835 9.08680484775 -6.23678765267 4.41881755284 -0.0285312500205 0.0343142334304 0.208186695622 -0.14738333835 -0.0131533367465 0.024974634844 -0.15584587277 0.359333315658 0.175333985768 0.239961169359 -0.0434810789337 0.00843121750967 0.21425389134 -0.0229256143036 0.274451134647 41.6453724924 56.4768836728 21.7177158868 17 3.51940164677 -2.63220966899 3.25129509427 4.41891321628 -4.36915556165 7.83467554231 -0.0696140798821 -0.023687291019 -0.0302588494287 -0.231901225157 0.171221057872 0.114032443278 0.0646670961401 0.0469514883639 -0.0786673220552 0.109524482901 -0.031409362582 0.011467097694 0.105656984697 -0.0321213706094 0.153499956709 40.9248466026 48.6008987158 21.2874446224 18 7.95607470671 -2.41556707558 3.84500131345 3.94797600125 -1.69170839977 4.7018564738 0.00473385414148 0.453871494564 0.164801237643 -0.685381734803 -0.326515733671 -0.253537167924 0.0872682482475 1.20630709798 -0.261585478313 0.0792524297552 0.00999000202 0.140231704916 0.421819681499 0.0300782427662 0.151461083754 48.3038138419 48.0739474257 14.3226351324
Refinement TLS group Show large table (4 x 18) Hide large table ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 chain 'H' and (resid 1 through 17 )2 X-RAY DIFFRACTION 2 chain 'H' and (resid 18 through 87 )3 X-RAY DIFFRACTION 3 chain 'H' and (resid 88 through 99 )4 X-RAY DIFFRACTION 4 chain 'H' and (resid 100 through 103 )5 X-RAY DIFFRACTION 5 chain 'H' and (resid 104 through 119 )6 X-RAY DIFFRACTION 6 chain 'H' and (resid 120 through 188 )7 X-RAY DIFFRACTION 7 chain 'H' and (resid 189 through 203 )8 X-RAY DIFFRACTION 8 chain 'H' and (resid 204 through 220 )9 X-RAY DIFFRACTION 9 chain 'L' and (resid 3 through 25 )10 X-RAY DIFFRACTION 10 chain 'L' and (resid 26 through 32 )11 X-RAY DIFFRACTION 11 chain 'L' and (resid 33 through 48 )12 X-RAY DIFFRACTION 12 chain 'L' and (resid 49 through 75 )13 X-RAY DIFFRACTION 13 chain 'L' and (resid 76 through 113 )14 X-RAY DIFFRACTION 14 chain 'L' and (resid 114 through 128 )15 X-RAY DIFFRACTION 15 chain 'L' and (resid 129 through 150 )16 X-RAY DIFFRACTION 16 chain 'L'